If you swap pads like that you should rebed them to get the old pad material off (Carbotech in this case) and the new pad material on the rotors.
And, as wtknght said, running on the track is hard on the fluid. I bleed after every session for this reason.
As an FYI, there is nothing wrong with swapping pads inside to outside. I do this all the time with mine to even wear (the inside pad wears slower as it is cooler).
